0_Microarray_Layout: contains files needed to design and analyze the STMV Patch-Probe 1x1M Agilent microarray.

1_RNA_Sequencing_Genewiz: contains data from GENEWIZ Sanger sequencing of the pSTMV plasmid cDNA.

2_Raw_Microarray_Images: contains raw microarray scan files in .tif format.
 - MS2: Scan of 8x60k array. MS2 RNA.
 - NormalU_Harvard: Scan of 1x1M array. STMV(+) RNA normal prep. Experiment conducted at Harvard.
 - NormalU_NoHeat_SDSU: Scan of 1x1M array. STMV(+) RNA prepared with no heat. Experiment conducted at SDSU.
 - NormalU_SDSU: Scan of 1x1M array. STMV(+) RNA normal prep. Experiment conducted at SDSU.
 - PseudoU_SDSU: Scan of 1x1M array. STMV(+) RNA transcribed with pseudoUridine. Experiment conducted at SDSU.
 - STMVm: Scan of 1x1M array. STMV(-) RNA normal prep. Experiment conducted at Harvard.

3_Feature_Extraction_Data: contains data from feature extraction in plain text format.

4_Inference_Data: contains results from Bayesian analysis of patch-probe data, in netCDF format.

5_Datasets: contains patch-probe data and metadata in netCDF format for several different experiments. These data files are produced from the plain text data files in the FeatureExtraction directory. These files can be loaded directly into an analysis program using a netCDF reader.

6_Patch_Binding: contains gel electrophoresis data for bulk patch binding, in CSV format.

7_RNAfold: contains data from RNAfold on STMV RNA and the pSTMV transcript sequences.
